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Workshop on Bio-Inspired Design of Networks

BIOWIRE 2007: Bio-Inspired Computing and Communication pp 19–32Cite as

Modelling Gene Regulatory Networks

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5151))

Abstract

We consider methods to compute analytical solutions for the probabilities of activation in gene regulatory networks with positive and negative feedback loops, similar to those introduced by René Thomas, and show how discrete state-space and continuous time probability models called can be used to compute their steady-state behaviour. The inclusion of logical dependencies in stochastic regulatory networks is the developed in detail.

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References

  1. Thomas, R.: Boolean formalisation of genetic control circuits. J. Theor. Biol. 42, 565–583 (1973)

    Article  Google Scholar 

  2. Thomas, R., Gathoye, A.M., Lambert, L.: A complex control circuit: regulation of immunity in temperate bacteriophages. Eur. J. Biochem. 71, 211–227 (1976)

    Article  Google Scholar 

  3. Thomas Thomas, R.: On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations. Springer Series in Synergetics, vol. 9, pp. 180–193 (1981)

    Google Scholar 

  4. Thomas, R.: Logical description, analysis and synthesis of biological and other networks comprising feedback loops. Adv. Chem. Phys. 55, 247–282 (1983)

    Google Scholar 

  5. Kaufman, M., Andris, F., Leo, O.: A Logical Analysis of T Cell Activation and Anergy. Proc. Natl. Acad. Sci. USA 96, 3894–3899 (1999)

    Article  Google Scholar 

  6. Thomas, R., Kaufman, M.: Multistationarity, the Basis of Cell Differentiation and Memory. I. Structural Conditions of Multistationarity and Other Non-Trivial Behaviour, and II. Logical Analysis of Regulatory Networks in Terms of Feedback Circuits, Chaos 11, 170–195 (2001)

    MATH  Google Scholar 

  7. Gelenbe, E.: Queueing networks with negative and positive customers. Journal of Applied Probability 28, 656–663 (1991)

    Article  MathSciNet  MATH  Google Scholar 

  8. Gelenbe, E.: G-networks with instantaneous customer movement. Journal of Applied Probability 30(3), 742–748 (1993)

    MathSciNet  MATH  Google Scholar 

  9. Gelenbe, E.: G-Networks with signals and batch removal. Probability in the Engineering and Informational Sciences 7, 335–342 (1993)

    Article  Google Scholar 

  10. Fourneau, J.M., Gelenbe, E., Suros, R.: G-networks with multiple classes of positive and negative customers. Theoretical Computer Science 155, 141–156 (1996)

    Article  MathSciNet  MATH  Google Scholar 

  11. Gelenbe, E., Fourneau, J.M.: G-Networks with resets. Performance Evaluation 49, 179–191 (2002)

    Article  MATH  Google Scholar 

  12. Fourneau, J.M., Gelenbe, E.: Flow equivalence and stochastic equivalence in G-Networks. Computational Management Science 1(2), 179–192 (2004)

    Article  MATH  Google Scholar 

  13. Gelenbe, E.: Learning in the recurrent random neural network. Neural Computation 5(1), 154–164 (1993)

    Article  MathSciNet  Google Scholar 

  14. Gelenbe, E., Pujolle, G.: Introduction to Networks of Queues, 2nd edn. J. Wiley & Sons, Chichester (1998)

    MATH  Google Scholar 

  15. Bernot, G., Comet, J.-P., Richard, A., Guespin, J.: Application of formal methods to biological regulatory methods: extending Thomas’ asynchronous logical approach with temporal logic. J. Theoretical Biology 229(3), 339–347 (2004)

    Article  Google Scholar 

  16. Bernot, G., Guespin-Michel, J., Comet, J.-P., Amar, P., Zemirline, A., Delaplace, F., Ballet, P., Richard, A.: Modeling, observability and experiment: a case study. In: Proc. Dieppe School on Modeling and Simulation of Biological Processes in the Context of Genomics, pp. 49–55. Frontier Group Pub. (2003) ISBN: 2-84704-036

    Google Scholar 

  17. de Jong, H., Geiselmann, J., Hernandez, C., Page, M.: Genetic analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 19(3), 336–344 (2003)

    Article  Google Scholar 

  18. Comet, J.-P.: De la bio-informatique textuelle à une approche formelle de la biologie des systèmes, Habilitation Thesis (Thèse d’Habilitation à diriger des Recherches), Université d’Evry-Val-d’Essonne, France, November 21 (2006)

    Google Scholar 

  19. Gelenbe, E.: Steady-state solution of probabilistic gene regulatory networks. Physical Review E 76(1), 031903 (2007); Virtual Journal of Biological Physics Research (September 15, 2007)

    Google Scholar 

  20. Gelenbe, E.: Network of interacting synthetic molecules in equilibrium. Proc. Royal Society A (Mathematical and Physical Sciences) (accepted for publication)

    Google Scholar 

  21. Gelenbe, E., Timotheou, S.: Synchronized interactions in spiked random networks. The Computer Journal (accepted for publication)

    Google Scholar 

  22. Gelenbe, E.: Network of interacting synthetic molecules in equilibrium. Proc. Royal Society A (Mathematical and Physical Sciences) (accepted for publication)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Intelligent Systems and Networks Group Department of Electrical and Electronic Engineering Department, Imperial College, London, SW7 2BT, UK

    Erol Gelenbe

Authors
  1. Erol Gelenbe
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Editor information

Editors and Affiliations

  1. The Computer Laboratory, University of Cambridge, William Gates Building, 15 JJ Thomson Avenue, CB3 0FD,, Cambridge, UK

    Pietro Liò

  2. Cambridge, UK

    Eiko Yoneki

  3. Cambridge University, UK

    Jon Crowcroft

  4. IBM TJ Watson Research Center, 704 Yorktown Heights, NY 10598, USA

    Dinesh C. Verma

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© 2008 Springer-Verlag Berlin Heidelberg

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Gelenbe, E. (2008). Modelling Gene Regulatory Networks. In: Liò, P., Yoneki, E., Crowcroft, J., Verma, D.C. (eds) Bio-Inspired Computing and Communication. BIOWIRE 2007. Lecture Notes in Computer Science, vol 5151. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92191-2_3

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  • DOI: https://doi.org/10.1007/978-3-540-92191-2_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-92190-5

  • Online ISBN: 978-3-540-92191-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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